Training activity information
Details
Analyse and interpret data to include fusion gene translocations and variant interpretation for:
- Ovarian
- Breast
- CNS
- Sarcoma
Type
Entrustable training activity (ETA)
Evidence requirements
Evidence the activity has been undertaken by the trainee repeatedly, consistently, and effectively over time, in a range of situations. This may include occasions where the trainee has not successfully achieved the outcome of the activity themselves. For example, because it was not appropriate to undertake the task in the circumstances or the trainees recognised their own limitations and sought help or advice to ensure the activity reached an appropriate conclusion.
Reflection at multiple timepoints on the trainee learning journey for this activity.
Reflective practice guidance
The guidance below is provided to support reflection at different time points, providing you with questions to aid you to reflect for this training activity. They are provided for guidance and should not be considered as a mandatory checklist. Trainees should not be expected to provide answers to each of the guidance questions listed.
Before action
What does success look like?
- Identify what is expected of you in relation to accurately analysing and interpreting genomic data, including fusion genes and variants, for, ovarian, breast, CNS, and sarcoma cases.
- Consider how the learning outcomes apply, specifically in relation to analyse, interpret reports of clinically relevant findings and interpret QC data.
- Discuss with your training officer to gain clarity of what is expected of you in relation to expectations for utilising bioinformatic pipelines and interpreting fusion detection data.
What is your prior experience of this activity?
- Think about what you already know about bioinformatic pipelines, variant calling, fusion detection, and interpreting genomic data in a clinical context.
- Consider possible challenges you might face during the activity, such as complex variants or ambiguous findings, and think about how you might handle them.
- Recognise the scope of your own practice for this activity i.e. know when you will need to seek advice or help, and from whom. You will need to seek advice from your Training Officer when required, for example when encountering highly complex or novel fusion gene translocations that challenge standard classification.
- Acknowledge how you feel about analysing and interpreting genomic data for these cancers.
What do you anticipate you will learn from the experience?
- Consider the specific skills you want to develop, such as analysing different types of genomic alterations (variants, fusions) using bioinformatic tools.
- Identify the specific insights you hope to gain into the clinical significance and interpretation guidelines for genomic findings in ovarian, breast, CNS, and sarcoma.
What additional considerations do you need to make?
- Consult actions identified following previous experiences of data analysis and interpretation.
- Identify important information you need to consider before embarking on the activity, such as relevant genomic databases, interpretation guidelines, and quality metrics for the data.
In action
Is anything unexpected occurring?
- Are you noticing anything surprising or different from what you anticipate whilst analysing and interpreting genomic data? Was this different from previous interpretation tasks?
- Are you encountering situations such as:
- Novel variants or complex rearrangements (e.g., in a Sarcoma case) that lack immediate reference in standard databases?
- Discrepancies between the sequencing data (variants) and the expected results based on the pathology report or clinical history?
- Ambiguous findings regarding a fusion gene translocation that challenges robust classification?
How are you reacting to the unexpected development?
- How is this impacting your actions? For example, are you responding to the situation appropriately? Did you immediately know how to proceed, or did you need to consult external resources or colleagues?
- Consider the steps you are taking in the moment, such as immediately running an alternative bioinformatic pipeline to confirm the presence of a complex rearrangement or consulting relevant guidelines for novel fusion interpretation.
- How are you feeling in that moment? For instance, did encountering this affect your confidence in your interpretation skills in that moment? Are you finding it difficult to adapt your analysis workflow?
What is the conclusion or outcome?
- Identify how you are working within your scope of practice. For example, are you successfully adjusting your analysis to confirm the data quality around the unexpected variant? Or are you needing support because the complex fusion gene translocation requires specialist bioinformatic review?
- What are you learning as a result of the unexpected development? For example, are you gaining immediate learning gained from navigating this particular challenge, such as a more robust technique for manually validating low-level fusion calls?
On action
What happened?
- Begin by summarising the key steps you took when analysing and interpreting the genomic data, focusing on fusion gene translocations and variant interpretation for the specific solid cancer case(s).
- Consider specific events, actions, or interactions which felt important, such as how you utilised bioinformatic tools to verify complex variants, or how you approached interpreting rare fusion genes in a sarcoma sample.
- Include any ‘reflect-in-action’ moments where you had to adapt to the situation as it unfolded, for instance, immediately consulting external databases or literature to verify the pathogenicity of an unexpected or novel variant encountered in an ovarian tumour case.
- How did you feel during this experience, e.g., did you feel focused on maintaining the factual integrity of the analysis or stressed by the ambiguity of a complex genomic alteration?
How has this experience contributed to your developing practice?
- Identify what learning you can take from this experience regarding analysis and interpretation. What strengths did you demonstrate, e.g., systematic approach to applying nomenclature and variant calling criteria?
- What skills and/or knowledge gaps were evident, e.g., difficulty applying bioinformatic pipelines to visualise complex fusion gene translocations?
- Compare this experience against previous engagement with similar activities – were any previously identified actions for development achieved? Has your practice improved in confidently interpreting fusion gene translocations or complex variants?
- Identify any challenges you experienced, such as needing to seek advice or clarification on scope of practice regarding the classification of a variant of unknown significance where clinical data was limited, and how you reacted to this.
What will you take from the experience moving forward?
- Identify the actions or ‘next steps’ you will now take to support the assimilation of what you have learnt, including from any feedback you have received, with regards to improving your interpretation of complex genomic aberrations.
- What will you do differently next time you approach data analysis, for instance, by proactively integrating quality metrics review earlier in the analysis phase to flag potential artefacts?
- Do you need to practise any aspect of the activity further, such as reviewing academic material on specific fusion genes (e.g., sarcoma) or enhancing your proficiency with specific bioinformatic analysis tools?
Beyond action
Have you revisited the experiences?
- How have your subsequent experiences of analysing and interpreting genomic data since completing this specific training activity led you to revisit your initial approach or decisions during that activity? For example, how a subsequent case involving a novel fusion gene translocation in a sarcoma sample forced you to re-evaluate the rigour of your initial bioinformatic pipeline filtering and manual review you applied during your first attempt at this training activity?
- Considering what you understand about data analysis, fusion detection, and variant interpretation now, were the actions or considerations you identified after your initial reflection on this training activity sufficient? How have you since implemented or adapted improvements in your analysis methodology or use of external interpretation databases based on further learning and experiences? For example, how you proactively implemented systematic checks against specific quality control metrics before finalising variant calls for breast cancer samples?
- Has discussing challenging variant interpretations or the integration of NGS quality metrics into analysis with colleagues, peers, or supervisors changed how you now view your initial experience in this training activity? For example, how professional storytelling with a senior colleague about a potential sequencing artefact initially mistaken for a pathogenic variant refined your understanding of the critical nature of meticulous QC review during analysis?
How have these experiences impacted upon current practice?
- How has the learning from this initial training activity, in combination with subsequent experiences, contributed to your overall confidence and competence in genomic analysis and interpretation, particularly in preparing for assessments like DOPS (performing tumour genotype analysis)? For example, how your accumulated ability in handling fusion gene analysis and applying nomenclature now enables you to confidently demonstrate the analytical steps using bioinformatic pipelines during a DOPS assessment?
- How has reflecting back on this specific training activity, combined with everything you’ve learned since, shaped your current approach to NGS data analysis? How does this evolved understanding help you identify when something is beyond your scope of practice or requires escalation? For example, how your evolved approach means you now routinely seek advice immediately when encountering complex, novel aberrations or findings that challenge existing classification guidelines?
- Looking holistically at your training journey, how has this initial experience, revisited with your current perspective, contributed to your development in analysing, interpreting, and preparing reports of clinically relevant findings?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 2 |
Outcome
Analyse, interpret and prepare interpretive reports of clinically relevant findings for patients with central nervous system (CNS), sarcoma tumours, and somatic and germline variants in ovarian and breast cancer. |
| # 4 |
Outcome
Interpret QC data including bioinformatic and NGS quality metrics in relation to assay performance, EQA and ISO:15189 standards. |